Exam 2, Biology 301D, 16 October 2002                     Printed name (required) ________________  

101 points possible

           

 

                                   

1. (4 pts.)

(2pts) Key Code: Fill in (A) and (B) on scantron question 1. to indicate your exam code.

 (2pts) Social security number and name. Bubble in the scantron with your name and your social security number (your SSN goes in the first 9 bubbles of the scantron ID field). 

NEW: Put your name on this hard copy, or you may not get credit for taking the exam.

 When finished, turn in both the Scantron and hard copy. You may write on this hard copy, but your grade will be determined by the Scantron form, provided we can find a hard copy from you.

None, one, all, or any combination of individual answers may apply to a question unless stated otherwise.  We use the acronym “NOM” for “None, One, or Many.”

As usual, phrases in italics may be taken as true.

 

Turn in your exams by the end of the hour.  A penalty may be assigned for late exams.
Current Events about Models (from the first lecture after exam 1)

2. (4 pts NOM) Which of the following points were raised about models and acrylamides?

(A)   Acrylamides are created by cooking certain foods to high temperature (especially fries, chips, and other carbohydrates) and are suspected of causing heart disease.

(B)   The models that have been used to assess the risk of acrylamides includes experiments with rats and occupational exposures to humans

(C)   On the basis of the current models for the health effects of acrylamides, the government has determined that the levels of acrylamides in fries and chips is harmful to humans. 

(D)   The rat model of the harmful effects of acrylamides has given different results than those obtained from humans, hence various scientists are wary of the results obtained from rats.

 

3. (4 pts NOM) Which points were made about models in breast cancer?

(A)  Recent work in molecular biology has found that there are at least 3-4 different types of breast cancer.

(B)   The recognition of multiple types of cancer within cancers that were formerly lumped under one type is likely to affect diagnosis and to improve treatment of cancers.

(C)   The value of the current method of screening for breast cancer (mammography) has been questioned because it yields many false positives.

 

Science and the Law

4. (6 pts NOM)  Which of the following technologies, as used in US courts or used by US government agencies, were said in class to be governed by regulations that require most (or all) features of ideal data? If an item was not discussed in class, do not fill it in.

(A)  hair matching (by means other than DNA)

(B)  dog sniffing matching of people and clothing

(C)  fingerprints (not DNA fingerprints, but real fingerprints)

(D)  DNA typing

(E)   Drug testing (as implemented by the Dept. of Transportation)

(F)   Polygraph (lie detection)


5. (8 pts NOM)  Which of the following points were presented in class as true?

(A) When fingerprint experts have been subjected to proficiency tests, their false positive rates ranged from 3% to over 20%.

(B) The large database of human fingerprints that have been maintained for years (by the FBI) has ensured low error rates in recent fingerprint analyses.

(C) A proficiency test is a test involving the use of standards.  It establishes a human and technical error rate.

(D) The routine use of DNA tests in the last few years of criminal investigation has shown that in approximately one of every four cases, the prosecution’s first choice of a “prime” suspect did not commit the crime.

(E) Since the death penalty was reinstated in 1976, slightly more than 1% of people sentenced to die have been released because they were later shown to be innocent by new evidence.  Although even this low percentage is disturbing, we have good reason to believe that this is a relatively accurate number of the total number of innocent people convicted to die.

(F) A very recent report by a government committee has declared that lie detection by polygraph (the old lie detector test) to be 98% accurate and thus supports its continued use.

(G) In 62 cases of convictions that were later overturned by DNA evidence, the most common factor leading to wrongful conviction was mistaken identity.

 

Data: Error

6-9. (4 pts each). For each of the following descriptions, indicate the types of error present (the italicized phrase identifies the error). Mark a type of error only if it is definitely present. Do not assume any more than what is explicitly mentioned in the problem. One answer and only one for each question.

 

(A)

(B)

(C)

(D)

(E)

Types of error:

Rounding, Precision and accuracy

Sampling

Human and technical

Bias

No error is indicated

 

6. (4 pts) Some old methods of DNA typing involved running two samples side-by-side on the same gel (e.g., a suspect sample and the forensic sample), and then measuring the bar code for each sample.  In some cases it was found that the technician reported that the two bar codes were the same when they were really slightly different from each other.  The cause of the erroneous “match” was that the technician knew what outcome was expected and made the measurements of one bar code while also looking at the other bar code.  What type of error is evident in the misreading of a bar code because the measurements were not made independently?  (one answer only)

(A)          (B)          (C)           (D)         (E)


7. (4 pts)  The scantron reader often scores options that have been erased.  Thus the scantron electronic file does not exactly match the answers on the paper scantron form.  What type of error is indicated by the difference between the paper scantron form and the electronic file?  (one answer only)

(A)          (B)          (C)           (D)         (E)

8. (4 pts) In many classes, teachers grade written exams and assignments knowing whose paper is being graded at the time.  It seems likely that, for some teachers (and we will assume so), students are graded somewhat unfairly whenever the teacher has already developed a sense of each student’s quality, because the teacher then assumes that good students know what they are writing about but that poor students don’t.  In other words, the teacher would assign a higher score to the “good” student than to the “bad” student for the same piece of work.  This problem would be avoided if the teacher was unaware of whose paper was being graded.  What type of error is indicated by the unfair scores?      (one answer only)

(A)          (B)          (C)           (D)         (E)

9. (4 pts) Clinical trials with vaccines or drugs are limited to a few thousand individuals.  A drug/vaccine that shows no complications in a clinical trial may nonetheless cause complications when it is used by millions (the rate of complications in the general population might be one per few-thousand people).  What type of error is indicated by the lack of even a single complication in the clinical trial but the observance of complications when the drug is released to the public?  (one answer only)

(A)          (B)          (C)           (D)         (E)

 

Ideal Data

 

10. (6 pts NOM)  In which of the following descriptions is a blind procedure present as pertains to the goal?  Do not assume more than the problem describes.  Fill in all options that describe a blind procedure or for which the answer is “yes.”  If the status of blind cannot be determined from the description, do not select that option.

(A)  The goal is to determine human and technical error rates through replication of individual samples.  Samples are coded before being sent for testing, and tubes containing the same sample have the same code.

(B)  Numbers are drawn from a hat to determine who is tested for drugs this month.  Samples are taken from the chosen individuals and sent to the lab.  Is the testing done blindly?

(C)  For written (typed) assignments, students draw a number at random.  They put that number as the only identifier on the assignment, and once it is graded, the students indicate which number belongs to them.  Is the grading done blindly?

(D)  A person reads their horoscope for the previous month and decides that most of what was supposed to happen did happen.  Is the reading done blindly?

(E)   Gregor Mendel (of genetics fame) crossed different pea plants and measured characteristics of both the parents and offspring to study inheritance.  He carefully kept track of which parents were used and which offspring were obtained from each cross, and he measured the offspring separately for each set of parents.  Were his measurements of offspring done blindly? 

(11-15). (4 pts each) For each of the following statements, mark the letters corresponding to the appropriate design features. Base your answer only on the information given. That is, mark a data feature only if it is explicitly present in the problem description.  Use only the options given in class or the book (At least one bubble, but possibly many bubbles = One or Many).

(A) explicit protocol

(C) standards

(E) blind

(B) replicates

(D) random

(F) None

11.  (4 pts OM).  Which features were identified as important in reducing bias?

                        (A)       (B)       (C)       (D)       (E)       (F)

12.  (4 pts OM).  Which features were identified as important in reducing sampling error?

                        (A)       (B)       (C)       (D)       (E)       (F)

13. (4 pts OM) The prosecution in a court case calls an expert witness to defend a new method of lie detection, based on brain waves measured when the person is asked questions.  This expert testifies that his method has been tested on 500 undergraduates who either deliberately told lies or told the truth about questions they were asked.  The design for the study had been submitted to the National Science Foundation and had been funded for $250,000 before it was carried out. Students were assigned to “truth” and “lie” groups based on which class in which they were registered, but even so, the person doing the analysis of brain waves was not aware of which students had been told to lie or tell the truth.  The expert witness said that the method had been able to correctly classify all truth-tellers and liars in the study.

                        (A)       (B)       (C)       (D)       (E)       (F)

14. (4 pts OM) A farmer wants to know if using pesticide will increase the amount of wheat harvested. To test this hypothesis, he applies the pesticide to each plot in his field that shows heavy pest infestation.. At the end of summer, the yield of wheat is compared between treated and untreated plots.  However, since all heavily-infested areas were treated and no lightly-infested area was treated, he finds himself in the unfortunate situation of not knowing whether the pesticide improved the crop yield.

(A)       (B)       (C)       (D)       (E)       (F)

15. (4 pts OM) A teacher wants to know if students learn more early in the morning than late in the morning.  So she teaches two sections of the same class, one at 08:00 and one at 11:00.  Only 50 students sign up for the 08:00 class, but 100 sign up for the 11:00 class.  She attempts to give the same lecture at both times, but finds that the second lecture is usually better because she has practiced it already that day.  However, she doesn’t bother to tell the students about her experiment, and as a consequence, many of the 08:00 students come to lecture at 11:00.  In the end, she is not able to reach a firm conclusion about learning and the time of day.

(A)       (B)       (C)       (D)       (E)       (F)

 


(16-18) (3 pts each). Do-it-yourself protocol. You are conducting an external review/test of a DNA lab. Your job is to send two tubes to the lab, with labels. There are several options for the content of and label on a tube. You must decide which contents to send and how to label the tubes so that the features of ideal data requested in the question are present from the lab's perspective. If a tube has a person's name on it, the lab can assume that the tube contents belong to the name of the person on the label. If a tube is labeled with a number, the contents are unknown to the lab but known to you. Your options for tube contents and tube labels are:

option

 tube label

Contents in the tube are from

ABO Blood type

Rh blood type

Gender

(A)

Sam Edwards

Sam Edwards

AB

+

Male

(B)

Chuck Berry

Chuck Berry

O

-

Male

(C)

Marty Ray

Marty Ray

O

+

Male

(D)

#13

Wanda Crill

A

-

Female

(E)

#21

John Crill

A

+

Male

(F)

June Scott

June Scott

B

+

Female

(G)

#101

June Scott

B

+

Female

(H)

#243

Linda Davis

O

-

Female

(I)

#17

Joel Sachs

AB

+

Male

(J)

No combination of tubes can satisfy the protocol

 

In the following questions, choose two letters among options (A)-(I) to describe the two tubes that will be sent to the lab. If it is possible to satisfy the protocol, the question will require exactly two letters and only two letters -- one for each tube. Thus, the answer for a question might be (A) & (B), or it might be (D) & (F). If more than one pair of options are possible correct answers, fill in only one correct pair of options. Thus, if (A) & (B) is one acceptable answer, and (C) & (D) is another acceptable answer, fill in either (A)&(B) or (C)&(D), but not both.   If a factor (such as identity, blood type, gender) is not specified in the protocol, then that factor will be ignored in grading the answer.  Alternatively, if a protocol cannot be satisfied with the options for tubes (A)-(I), fill in (J). 

16. (3 pts) Choose two tubes to guarantee replication of ABO and Rh blood type without replication of person.

two tubes:                     (A)       (B)       (C)       (D)       (E)       (F)        (G)       (H)       (I)        (J)

17. (3 pts) The lab has a way to identify the gender (sex) of a sample. Make the protocol fully blind to the lab and replicated for gender but not replicated for an individual or for either blood type.

two tubes:                     (A)       (B)       (C)       (D)       (E)       (F)        (G)       (H)       (I)        (J)

18. (3 pts) Make the protocol fully blind to the lab and not replicated in any way (not for gender, either blood type, nor individual).

two tubes:               (A)       (B)       (C)       (D)       (E)       (F)        (G)       (H)       (I)        (J)

 19. (4 pts NOM).  Which of the following are true?

(A)  A study can be randomized in some respects but not others.

(B)  A study can be blind in some ways but not others.

(C)  A study can be replicated in some ways but not others.

(D)  A study can completely lack blind features, randomization, and standards.

(E)   No study can be replicated in all respects.   

Drug Testing

(20, 21). (4 pts each)  Each of items (A) through (G) describes a feature of Department of Transportation drug tests.  The details of the drug testing rules are presented in the Federal Register 49 CFR PART 40 and described in a 100+ page pamphlet "Guidelines for Implementing the FHWA anti-drug program."

(A) Each manager whose employees are tested is required to include 3 known blank samples (lacking drugs) for every 100 unknowns; managers with more than 2000 drivers must also include some samples known to contain drugs.

(B) The laboratory initially tests all samples with a rapid screen; positive samples are retested more comprehensively.

(C) When a sample is sent to the laboratory for testing, it is labeled with a code, rather than the name of the person being tested.

(D) Split sample collection is required -- the partitioning of the original sample into two vials -- so that the second sample can be retained for retesting.

(E) The rules specify that any retesting (in the event of a positive sample) is to be done by a different laboratory than did the original test.

(F) The regulations require that any driver involved in an accident be tested for drugs and alcohol.

(G) Lab results are sent to the medical review officer before being returned to the office originating the test.

     

20. (4 pts) Which feature(s) represent standards in some part of the drug-testing protocol, even when retesting is not done? (none, one, or many)

(A)       (B)       (C)       (D)       (E)       (F)        (G)                  

 

21. (4 pts) Which feature(s), if followed, ensure that DOT drug tests of an individual's sample are done blind? (none, one, or many)

(A)       (B)       (C)       (D)       (E)       (F)        (G)                  

 

DNA Typing

22. (4 pts)  It was suggested in class that lab error rates from such problems as sample mixup are still on the order of 1% in modern DNA typing.  Consider a trial in which the lab has declared a match, with a random match probability of 1/billion; but it is also known that the lab makes a mistake 1% of the time in declaring a match.  How should the jury’s calculation of the significance of the match be affected by the lab error rate? (NOM)

(A)  The lab error rate does not affect the calculation, because by the time the data are presented at trial, lab errors have been corrected.

(B)  The lab error rate does not affect the calculation, because the random match probability has already taken lab error into account.

(C)  The lab error rate affects the calculation in a minor way.  The proper correction is to multiply the probability that no lab error occurred (which is 0.99) times the random match probability (1/billion) to get the corrected value, which is still nearly 1/billion.

(D)  The lab error rate affects the calculation in a major way.  There is a 1% chance that the sample did not come from the suspect because of lab error, plus a 1/billion chance that the sample did not come from the suspect because of a random match to someone else.  Overall, there is approximately a 1% chance that the sample did not come from the suspect – the calculation is dominated by the lab error rate.

23. (4 pts NOM).  Which exceptions to ideal data were evident in the DNA analysis of the Castro Case (as per the book)?

(A)              lack of blind analysis

(B)              lack of standards

(C)              lack of randomization

(D)              lack of replication

(E)               Violation of protocol

24.(4 points NOM)  Which facts about modern DNA typing are true?

(A)  When done properly, DNA results have a low probability of producing a chance or random match between the forensic sample and a person not associated with the crime.  This probability is often less than 1/million.

(B)  DNA typing can be performed from most tissues and needs only trace amounts of tissue.  For example, enough DNA can be recovered from the back of a postage stamp or a baseball bat handle to determine whether a particular suspect licked the stamp or held the bat.

(C)   The use of PCR (“Xeroxing” DNA) has allowed tests on small forensic samples of DNA to be replicated many times.

(D)  Current lab errors are largely caused by problems with DNA typing machines and are likely to become much less common as better equipment is developed.